Multilocus variable-number of tandem-repeats analysis of Salmonella enterica serotype Gallinarum and comparison with pulsed-field gel electrophoresis genotyping

Salmonella enterica serovar Gallinarum is the causative agent of fowl typhoid, a severe disease of poultry, responsible for heavy economic losses. Epidemiologic investigation of fowl typhoid significantly benefits from molecular typing tools, RAPD and PFGE have been proposed for this purpose. PFGE, a well established technique, is still the gold standard among typing methods for most bacteria, including salmonella. Nevertheless, it has some limitations regarding execution and reproducibility, in particular it is labour intensive and requires good technical expertise. Furthermore, it needs accurate standardization and results can be ambiguous to interpret. Such limitations can hamper reproducibility and transfer of results. As a possible alternative to PFGE, multilocus variable-number of tandem-repeats analysis (MLVA) has recently emerged as an effective genotyping method for many bacterial pathogens showing high discriminatory power associated to robustness. We developed a six-loci MLVA protocol for Salmonella Gallinarum and compared it to PFGE performed with SpeI, XbaI and NotI on fifty isolates. The proposed MLVA has a high discriminatory power, equivalent to that of the three-enzyme PFGE (Simpson's index 0.94 for MLVA, 0.93 for three-enzyme PFGE) but it is simpler to perform and straightforward in genotype identification, allowing unambiguous exchange of results. Stability of selected VNTR loci, assessed in vitro and in vivo, is good but not absolute, reflecting the sensitivity of MLVA to detect evolutionary changes of bacteria. Clustering of the isolates as determined by MLVA typing is substantially confirmed by PFGE.     

大雁、斑头雁和天鹅源沙门氏菌血清及脉冲场凝胶电泳分型研究

为了解大雁、斑头雁及天鹅源沙门氏菌流行特征和脉冲场凝胶电泳（PFGE）分型,本研究对33株沙门氏菌进行血清型鉴定,采用PFGE对其进行基因分型,并用BioNumerics 6.6软件进行聚类分析。鉴定出丙型副伤寒沙门氏菌6株、汤卜逊沙门氏菌19株、乙型副伤寒沙门氏菌1株、伊鲁木沙门氏菌1株、奥斯陆沙门氏菌1株、5株未定型。PFGE聚类分型共分为16个型别,其相似度为53.7%~100.0%,且大多数菌株与人源菌株相似度超过80%。结果表明,大雁、斑头雁及天鹅源沙门氏菌相同血清型PFGE带型高度相似,可能来自同一克隆株,不同血清型PFGE带型差别较大。     

PFGE Genotyping and Serotype Analysis of Salmonella Isolated from Goose,Anserindicus and Cygnus

To understand the Salmonella epidemic characteristics and pulsed field gel electrophoresis（PFGE）genotyping of goose,Anserindicus and Cygnus,33 strains of Salmonella were serotype typed by PFGE and genotyped with BioNumerics 6.6 cluster analysis software.The results showed that there were 16 PFGE patterns,which displayed 6 strains Salmonella paratyphi C,19 strains Salmonella thompson,1 strains Salmonella paratyphi B,1 strain Salmonella irumu,1 strain Salmonella oslo,5 undifferentiated.PFGE similarity is about 53.7% to 100.0%,and most of the strains and anthropogenic strains similarity was more than 80%.The results showed that goose,Anserindicus and Cygnus Salmonella serotypes same PFGE type with a high degree of similarity,and possibly from the same clone,quite different serotypes PFGE band pattern difference.     

Molecular characterisation of avian Pasteurella multocida isolates from Australia and Vietnam by REP-PCR and PFGE

A total of 95 isolates of Pasteurella multocida were analysed by pulsed field gel electrophoresis (PFGE) using the enzyme ApaI, including 73 avian isolates from Australia and 22 from Vietnam. The majority of field isolates were capsular Type A, with the predominant somatic serovars of 1, 3, 4 and 3,4. Twenty-one distinct profiles were evident among the Australian isolates, with only 3 profiles observed among the 22 P. multocida strains isolated from Vietnam. Within the Australian isolates, related and unrelated outbreaks could be identified by PFGE. These results correlated well with previously published studies, with greater discrimination shown by PFGE. Repetitive extragenic palindromic sequence PCR (REP-PCR) analysis of representative isolates from PFGE classifications yielded 21 profiles, with most of the subgroups in accordance with PFGE analysis. While REP-PCR was shown to be less discriminating than PFGE, the epidemiological relatedness of strains compared favourably between the techniques. Thus, the ease and rapidity of REP-PCR while maintaining a high level of differentiation, supports the use of REP-PCR as a competent alternative to the more labour-intensive PFGE system for strain identification and epidemiological studies of avian P. multocida.     

Molecular Differentiation of Mycoplasma gallisepticum and Mycoplasma imitans Strains by Pulsed‐Field Gel Electrophoresis and Random Amplified Polymorphic DNA

Pulsed‐field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) analysis were used to compare 21 Mycoplasma gallisepticum strains and five M. imitans strains. Each strain of M. gallisepticum typed by PFGE and RAPD methods was genetically quite unique and RAPD and PFGE fingerprinting enabled strain characterization. Relationships between the M. gallisepticum and M. imitans strains were established and dendrograms were drawn from PFGE and RAPD patterns. PFGE group A and RAPD group D were significantly associated with M. imitans strains (P < 0.05). Three M. imitans strains shared the same PFGE and RAPD patterns. The two M. gallisepticum vaccine strains had singular PFGE and RAPD patterns. Thus, PFGE and RAPD can be used to investigate disease outbreaks in vaccinated flocks or for epidemiological tracking. For M. gallisepticum, the RAPD and PFGE discriminatory powers were superior to 0.95 and the in vitro, in ovo and in vivo reproducibility of RAPD and PFGE was 100%. The RAPD drawback was the inconsistent band intensity complicating the interpretation of patterns, while the PFGE limit was its low typeability (86%). Thus, these two molecular typing methods seemed complementary for M. gallisepticum epidemiological studies.     

Spatio‐Temporal Scan Statistics for the Detection of Outbreaks Involving Common Molecular Subtypes: Using Human Cases of Escherichia coli O157:H7 Provincial PFGE Pattern 8 (National Designation ECXAI.0001) in Alberta as an Example

Molecular typing methods have become a common part of the surveillance of foodborne pathogens. In particular, pulsed‐field gel electrophoresis (PFGE) has been used successfully to identify outbreaks of Escherichia coli O157:H7 in humans from a variety of food and environmental sources. However, some PFGE patterns appear commonly in surveillance systems, making it more difficult to distinguish between outbreak and sporadic cases based on molecular data alone. In addition, it is unknown whether these common patterns might have unique epidemiological characteristics reflected in their spatial and temporal distributions. Using E. coli O157:H7 surveillance data from Alberta, collected from 2000 to 2002, we investigated whether E. coli O157:H7 with provincial PFGE pattern 8 (national designation ECXAI.0001) clustered in space, time and space–time relative to other PFGE patterns using the spatial scan statistic. Based on our purely spatial and temporal scans using a Bernoulli model, there did not appear to be strong evidence that isolates of E. coli O157:H7 with provincial PFGE pattern 8 are distributed differently from other PFGE patterns. However, we did identify space–time clusters of isolates with PFGE pattern 8, using a Bernoulli model and a space–time permutation model, which included known outbreaks and potentially unrecognized outbreaks or additional outbreak cases. There were differences between the two models in the space–time clusters identified, which suggests that the use of both models could increase the sensitivity of a quantitative surveillance system for identifying outbreaks involving isolates sharing a common PFGE pattern.     

Automated ribotyping, a rapid typing method for analysis of Erysipelothrix spp. strains

Automated ribotyping classified 70 Erysipelothrix species strains, previously classified into 14 RAPD patterns and into 63 PFGE patterns, into 27 ribogroups. Twenty-three strains of the 70 analyzed and classified into 13 ribogroups were previously classified into six ribotypes by the traditional ribotyping method. Moreover, automated ribotyping differentiated seven strains that were not differentiated by PFGE. Therefore, automated ribotyping was more sensitive than RAPD and traditional ribotyping, and it might be a useful method for a rapid screening in epidemiological study of strains of this genus, and more accurate results can be obtained when this method is used together with PFGE.     

Biofilm production by Staphylococcus aureus associated with intramammary infection

Biofilm production by 221 Staphylococcus aureus isolates from 45 dairy herds was evaluated. Isolates were from composite milk of 117 cows, from teat skin of 70 cows, and from 34 milking machine unit liners. Of S. aureus from milk samples, 41.4% were biofilm producers, as compared to 24.7 and 14.7% of the isolates collected from skin and liners. Pulsed field gel electrophoresis (PFGE) best categorized S. aureus biofilm producers as compared to phage typing and binary typing. PFGE types that were significantly associated with isolation from milk as opposed to teat skin or liners, had isolates that were more likely to produce biofilm than PFGE types that were isolated from milk, skin and liners at similar frequencies. By contrast, PFGE type A was significantly associated with isolation from teat skin and had few biofilm producers. PFGE type Q, which is exclusively a milk, isolate produced more biofilm as evidenced by absorbance values. Given S. aureus that are associated with milk are more likely to produce biofilm as compared to extramammary sources (teat skin and milking unit liners), suggests that biofilm production is a risk factor for infection.     

The Limitations of Pulsed‐Field Gel Electrophoresis for Analysis of Yersinia enterocolitica Isolates

This study describes the analysis of 432 isolates of Yersinia enterocolitica by pulsed‐field gel electrophoresis (PFGE). PFGE had a high level of discrimination with biotype 1A isolates (Simpson's Diversity Index 0.997), but with the clinically important biotypes 2, 3 and 4, the discriminatory ability of PFGE was so low as to severely limit its usefulness (DI <0.6). For biotypes 2, 3 and 4, 79% or more of isolates of each biotype were of just three different PFGE profiles. Because of this, four known outbreaks of yersiniosis would not have been identified by PFGE analysis. However, a previously unrecognized potential outbreak of yersiniosis caused by biotype 4 isolates was identified on the basis of a rare PFGE genotype with spatial and temporal clustering. We conclude that PFGE has a very limited application to the genotyping of Y. enterocolitica biotypes 2, 3 and 4, and inferences based on finding indistinguishable PFGE profiles among cases or between cases and sources need to be substantiated using alternative typing tools, or strong epidemiological evidence.     

Improvement and validation of RAPD in combination with PFGE analysis of Salmonella enterica ssp. enterica serovar Senftenberg strains isolated from feed mills

In 1995 and 1996 a Swedish feed mill had problems due to a persistent contamination of Salmonella enterica spp. enterica serovar Senftenberg that was difficult to eliminate. Forty-eight strains isolated from the feed mill, together with unrelated strains included to evaluate the discriminatory power and reproducibility, were analysed by pulsed-field gel electrophoresis (PFGE). The source of contamination in the feed mill was identified and preventative measures were taken, that led to a resolution of the problem. A previously developed randomly amplified polymorphic DNA (RAPD) protocol was used, to evaluate a rapid and low-cost alternative to PFGE typing. The use of the alternative thermostable DNA polymerase Tth was shown to increase the reproducibility of the RAPD analysis. The reproducibility, in terms of Pearson's and Dice's similarity coefficients for duplicate runs, increased from 72.0 +/- 16.9% and 72.3 +/- 12.9% for Taq to 91.6 +/- 7.5% and 90.9 +/- 5.3% for the fingerprints obtained for the RAPD method employing Tth DNA polymerase. Simpson's index of diversity was calculated and found to be 0.580 for RAPD and 0.896 for PFGE. All of the seven RAPD types could be subdivided into one or more PFGE types, whereas none of the 22 PFGE types was divided into more than one RAPD type. RAPD provides a simple, rapid and powerful screening method that can be used to initially select isolates for further analysis by PFGE.     

PFGE and PCR/RFLP typing of Campylobacter jejuni strains from poultry

1. Pulsed-field gel electrophoresis (PFGE) and PCR-restriction fragment length polymorphisms of the flagellin gene (fla-RFLP) were used to analyse 92 poultry and 110 human strains of Campylobacter jejuni. 2. Among poultry strains, 11 fla-RFLP and 11 PFGE subtypes were found, while human strains could be divided into 23 fla-RFLP and 32 PFGE subtypes. Altogether, 31 fla-RFLP and 32 PFGE subtypes were found. 3. The results show that individual flocks in farms are mostly infected with a single C. jejuni clone, while during subsequent colonisation their genotypes altered. fla-RFLP and PFGE profiles in poultry and humans were identical in less than 6% of cases. The results found so far confirm previous findings that chicken meat does not represent as important a source of campylobacteriosis as was previously believed. 4. The typing of Campylobacter sp. forms the basis for an evaluation of the current state and risk assessment of various Campylobacter sp. sources in relation to humans. Examination of samples with only one method is insufficient for epidemiology studies, because apparently different clones identified with one method could originate from a single clone, which could be proved with the other method.     

Genotypic characterisation by PFGE of Salmonella enterica serotype Enteritidis phage types 1, 4, 6, and 8 isolated from animal and human sources in three European countries

A total of 101 strains of Salmonella Enteritidis phage types (PT) 1, 4, 6, and 8 from Denmark, England and Spain were studied by PFGE to elucidate genetic relationships among strains isolated from animal, human and environmental sources between 1983 and 1997. Analysis with Xba I, Bln I and Spe I enzymes showed that the power of discrimination of this method was increased by the combination of the three enzymes (D=0.802), subdividing the strains into 28 genomic groups or genotypes. Many of the PT1, PT4, and PT6 strains from the three countries shared the same PFGE combination profile A1-A1-A1, confirming the close relationship among these phage types and the protracted spread of a single clone over a large geographical area. In general, strains from Denmark showed more variation in their PFGE profiles than those from England and Spain. PT4 strains exhibited genetic homogeneity in the three countries independently of their sources and period of isolation. Spe I gave the highest index of discrimination among PT6 strains as evidenced by a variety of PFGE profiles. The data clearly confirmed that PT8 strains isolated in the three countries were of a unique clonal origin, and the PFGE combination profile A10-A10-A1 was predominant and specific for this phage type. It is concluded that PFGE, in combination with phage typing, represents a suitable tool for the epidemiological typing of Salmonella Enteritidis strains which could be used for investigations or surveillance of the international spread of these clones.     

脉冲场凝胶电泳技术在猪链球菌分型中的应用

脉冲场凝胶电泳是一种可用于分离20 kb至10 Mb大分子质量DNA的新型凝胶电泳技术。该法应用于猪链球菌的分子分型,通过观察电泳条带的差异,为确定菌株之间的亲缘关系,分析基因型和临床症状之间的关系等方面提供了可靠的技术手段。文章介绍了脉冲场凝胶电泳技术的应用状况及猪链球菌的分型现状,并阐述了该技术在猪链球菌分子分型研究方面的应用及发展前景。     

Molecular genotyping of Salmonella enterica Abortusovis by pulsed field gel electrophoresis

Genotyping of Salmonella strains is an important tool to discriminate among isolates and to improve epidemiological studies when an outbreak occurs. No phagetyping scheme is available for Salmonella enterica subsp. enterica serovar Abortusovis (SAO) and molecular methods previously used were not standardized and were time consuming. Among the DNA-based methods of genotyping, pulsed field gel electrophoresis (PFGE) is currently in use to subtype Salmonella isolates. In this study we evaluated the feasibility of genotyping of SAO by XbaI and BlnI restrictions. Separation of restricted fragments was performed by PFGE. To test the possibility to apply this methodology to epidemiological investigation, a collection of 38 SAO strains isolated in different regions of Italy were analyzed. Eighteen and 29 different PFGE profiles were defined for XbaI and BlnI digestions, respectively. The method demonstrated an adequate typing ability and an excellent discriminatory power. Results from this study show that PFGE may represent a powerful tool to discriminate within the SAO serovar, and provide useful information in support of traditional epidemiological investigations. In particular, this method could be used to identify the origin of infection during outbreaks within a single flock or in different herds.     

Genomic relatedness among Actinobacillus pleuropneumoniae field strains of sterotypes 1 and 5 isolated from healthy and diseased pigs.

Forty-four Actinobacillus pleuropneumoniae isolates recovered from both healthy and diseased pigs were characterized by random amplified polymorphic DNA analysis (RAPD), pulsed field gel electrophoresis (PFGE) and apx toxin gene typing. Nine RAPD types and 14 PFGE patterns were identified. No common RAPD or PFGE patterns were found between strains of serotype 1 and those of serotype 5. The RAPD analysis indicated that the 15 serotype 1 strains isolated from diseased pigs were assigned to 4 RAPD types, with 66% of strains characterized by the same RAPD type. By contrast, the 5 strains of serotype 1 isolated from healthy carriers were dispersed in 4 RAPD types. These data suggest that the diversity of strains isolated from healthy pigs could be higher than that of strains recovered from diseased pigs. In addition, all serotype 5 strains exhibited a unique RAPD type. Unlike RAPD, PFGE analysis allowed discrimination among isolates of serotype 1 and among those of serotype 5. All but 3 isolates showed the same apx genotype as their respective serotype reference strain. These data indicate that RAPD analysis is a valuable rapid tool for routine subtyping of strains of serotype 1. For strains of serotype 5, a combination of several typing methods, such as PFGE and apx gene typing, is needed to provide useful information on the molecular epidemiology of swine pleuropneumonia.     

Genetic fingerprinting (PFGE) of bacterial isolates for their molecular epidemiology

The determination of fragment patterns of bacterial genomic DNA after digestion with long-range-cutting restriction enzymes and their separation in pulsed-field-gelelectrophoresis is currently regarded as reliable fingerprinting tool for surveillance and identification of infectious sources and routes of bacterial pathogens. The PFGE based molecular fingerprinting has been applied and used for a broad range of bacterial species. As a prerequisite for its application in national and international network studies (German PulseNet, PulseNet USA, Salmgene) a common protocol for rapid production (1-2 days) of standardised and electronically readable fragment patterns has been developed. National and international outbreaks, diffuse outbreaks and long term surveillance of the ups and downs of pathogens have been successfully carried out by means of PFGE studies. The international outbreak of Salmonella enterica serovar Oranienburg (2001) due to contaminated chocolate is described here underlining the usefulness of PFGE as genetic fingerprinting for epidemiological purposes.     

The diversity of Mycoplasma hyopneumoniae within and between herds using pulsed-field gel electrophoresis

Over the years, pulsed-field gel electrophoresis (PFGE) has been proven a robust technique to type isolates with a high resolution and a good reproducibility. In this study, a PFGE protocol is described for the typing of Mycoplasma hyopneumoniae isolates. The potential of this technique was demonstrated by comparing M. hyopneumoniae isolates obtained from the same as well as from different herds. The use of two different restriction enzymes, SalI and ApaI, was evaluated. For each enzyme, the resulting restriction profiles were clustered using the unweighted pair group method with arithmetic means (UPGMA). For both obtained dendrograms, the included isolates of the related M. flocculare species clustered separately from all M. hyopneumoniae isolates, forming the root of the dendrograms. The PFGE patterns of the M. hyopneumoniae isolates of different herds were highly diverse and clustered differently in both dendrograms, illustrated by a Pearson's correlation coefficient of only 0.33. A much higher similarity was observed with isolates originating from different pigs of a same herd. The PFGE patterns of these isolates always clustered according to their herd and this for both dendrograms. In conclusion, the results indicate a closer relationship of M. hyopneumoniae isolates within a herd compared to isolates from different herds and this for both restriction enzymes used. Since the described PFGE technique was shown to be highly discriminative and reproducible, it will be a helpful tool to further elucidate the epidemiology of M. hyopneumoniae.     

Identification of patterns of transmission of Salmonella within swine production systems using pulsed field gel electrophoresis (PFGE) and repetitive sequence polymerase chain reaction (REP-PCR): a quantitative analysis

Pulsed field gel electrophoresis (PFGE) using 3 enzymes (Spe I, Xba I, Avr II) and repetitive sequence polymerase chain reaction (REP-PCR) with 3 primers (BOX, ERIC, REP) were compared with respect to their validity as a method for identifying transmission of Salmonella on swine farms. Sixty-eight isolates of Salmonella were obtained from feces of swine, cats, mice, and birds, insect body parts, water and floor samples, and boot scrapings collected on 9 swine farms in Illinois USA. Genetic distances between isolates were calculated using the Dice matching coefficient. Cluster analysis of distance matrices was conducted using the UPG-MA algorithm. There was no significant difference between PFGE and REP-PCR in the genetic diversity detected; however, REP-PCR differentiated between 14 pairs of isolates which PFGE identified as identical. There were no significant differences between PFGE and REP-PCR in identifying all or most close genetic links as isolates from the same farm, the same building, and from the same sampling visit, suggesting ecological validity for both methods. Thus, REP-PCR should be considered as an acceptable and perhaps preferable alternative to PFGE as a genotyping method for studies of Salmonella transmission.     

Pulsed-field gel electrophoresis typing of Campylobacter fetus subsp. fetus isolated from sheep abortions in New Zealand

AIMS: To genotype Campylobacter fetus subsp. fetus isolates cultured from sheep abortions submitted to diagnostic laboratories in New Zealand during the year 2000 breeding season. To compare the types found nationally with those found in the Hawke's Bay region in 1999, and strains held in the New Zealand Reference Culture Collection, Medical Section (NZRM) from a study published in 1987. METHODS: Campylobacter fetus subsp. fetus isolates cultured by veterinary diagnostic laboratories in the year 2000 breeding season, from sheep abortions from throughout New Zealand, were typed using pulsed-field gel electrophoresis (PFGE). In addition, seven freeze-dried C. fetus subsp. fetus isolates (strain numbers 2939-2945) from the NZRM, representing restriction types a-g found amongst sheep abortion isolates in a study published in 1987, were typed using PFGE. RESULTS: In total, 293 C. fetus subsp. fetus isolates from 200 farms were obtained from veterinary diagnostic laboratories. Twenty-two distinct PFGE profiles were identified amongst the isolates. PFGE type B1 was predominant in each region of New Zealand and was identified from 66% of farms overall. Of the C. fetus subsp. fetus restriction types a-g lodged with the NZRM, 3/7 had PFGE profiles indistinguishable from profiles found in the current study. The other four restriction types had PFGE profiles that were unique but similar to those found in the current study. CONCLUSIONS: PFGE type B1 was predominant amongst the C. fetus subsp. fetus isolates cultured from sheep abortions in each region of New Zealand in the year 2000, as was found in Hawke's Bay in 1999. The similarity between PFGE profiles of C. fetus subsp. fetus sheep abortion isolates from 1987 and 2000, and the relative prevalence of the PFGE groups, suggests that there has been no major genotypic shift in the population of C. fetus subsp. fetus implicated in sheep abortion in New Zealand during this time.     

Pulsed field gel electrophoresis for animal Salmonella enterica serovar Typhimurium isolates in Taiwan

Salmonella enterica subspecies enterica serovar Typhimurium is a common pathogen for humans and animals. In order to trace the clonal relationship and to find the circulating strains between human and animal isolates, chromosomal DNAs from 87 serovar Typhimurium strains isolated from animals (pigs were the majority) were subjected to XbaI and SpeI digestion and pulsed field gel electrophoresis (PFGE). For the 87 animal isolates, 38 PFGE pattern combinations were obtained. As the subtyping results from animal isolates were compared with those from the 45 human isolates, it was found that 14 of the animal isolates and 13 of the human isolates shared a common PFGE pattern combination, i.e., pattern XgSf (or called X5S4). When these human and animal isolates were subjected to antibiotic susceptibility test using 11 antibiotics, it was found that strains of pattern XgSf (X5S4) belong to a common antibiogram pattern which is tetracycline, gentamicin, ampicillin, streptomycin and chloramphenicol resistant. Since most of the animal and human strains in pattern XgSf were originally isolated from various areas over different years, strains of this PFGE pattern may be the most epidemic strains which circulating between human and animal sources.